Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
Genes (Basel). 2023 Sep 26;14(10):1871. doi: 10.3390/genes14101871.
Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes, and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In this study, we used single-cell multiomic analysis to profile the transcriptome and epigenome of MSC from four healthy donors. Data were obtained from ~1300 to 1600 cells for each donor. These cells were clustered into four groups, indicating that MSC from different donors have distinct chromatin accessible regulatory elements for regulating gene expression. To investigate the mechanism by which MSC undergo osteogenic differentiation, we used the chromatin accessibility data from the single-cell multiome data to identify individual-specific enhancer-promoter pairs and evaluated the expression levels and activities of the transcriptional regulators. The MSC from four donors showed distinct differentiation potential into osteoblasts. MSC of donor 1 showed the largest average motif activities, indicating that MSC from donor 1 was most likely to differentiate into osteoblasts. The results of our validation experiments were consistent with the bioinformatics prediction. We also tested the enrichment of genome-wide association study (GWAS) signals of several musculoskeletal disease traits in the patient-specific chromatin accessible regions identified in the single-cell multiome data, including osteoporosis, osteopenia, and osteoarthritis. We found that osteoarthritis-associated variants were only enriched in the regions identified from donor 4. In contrast, osteoporosis and osteopenia variants were enriched in regions from donor 1 and least enriched in donor 4. Since osteoporosis and osteopenia are related to the density of bone cells, the enrichment of variants from these traits should be correlated with the osteogenic potential of MSC. In summary, this study provides large-scale data to link regulatory elements with their target genes to study the regulatory relationships during the differentiation of mesenchymal stem cells and provide a deeper insight into the gene regulatory mechanism.
间充质干细胞（MSC）是多能干细胞，可分化为多种细胞类型，包括成骨细胞、软骨细胞和脂肪细胞。骨质疏松症发展过程中成骨细胞分化减少，导致骨形成减少。此外，来自不同供体的 MSC 具有不同的成骨能力。在这项研究中，我们使用单细胞多组学分析对来自四位健康供体的 MSC 的转录组和表观基因组进行了分析。每位供体的数据来自约 1300 到 1600 个细胞。这些细胞被聚类为四个组，表明来自不同供体的 MSC 具有不同的染色质可及性调控元件，用于调节基因表达。为了研究 MSC 经历成骨分化的机制，我们使用单细胞多组学数据中的染色质可及性数据来鉴定个体特异性增强子-启动子对，并评估转录调控因子的表达水平和活性。四位供体的 MSC 显示出不同的向成骨细胞分化的潜力。供体 1 的 MSC 显示出最大的平均基序活性，表明供体 1 的 MSC 最有可能分化为成骨细胞。我们的验证实验结果与生物信息学预测一致。我们还测试了全基因组关联研究（GWAS）信号在单细胞多组学数据中鉴定的患者特异性染色质可及区域中的几种肌肉骨骼疾病特征的富集，包括骨质疏松症、低骨量和骨关节炎。我们发现，骨关节炎相关变体仅在从供体 4 中鉴定的区域中富集。相比之下，骨质疏松症和低骨量变体在供体 1 的区域中富集，在供体 4 中最少富集。由于骨质疏松症和低骨量与骨细胞密度有关，这些特征的变体富集应该与 MSC 的成骨潜力相关。总之，这项研究提供了大规模的数据，将调控元件与其靶基因联系起来，以研究间充质干细胞分化过程中的调控关系，并深入了解基因调控机制。
